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Messages - VoxRat

1
In fact the whole Third Way movement got started because many scientists are finally beginning to realize this.
Nope.

Since you've never read a single book by any "Third Wayer" this, obviously, expresses nothing more than your wishful thinking.
Nope.

Here's Shapiro way back in 1997 ...
Quote
Localized random mutation, selection operating
"one gene at a time" (John Maynard Smith's formulation), and gradual modification of
individual functions are unable to provide satisfactory explanations for the molecular data, no
matter how much time for change is assumed. There are simply too many potential degrees of
freedom for random variability and too many interconnections to account for. http://shapiro.bsd.uchicago.edu/Shapiro.1997.BostonReview1997.ThirdWay.pdf

Since that time many have joined him.


But that does not say anything about whether
Quote
... errors under my definition are necessary to ensure long lineages.

There certainly ARE other things going on, beyond just nucleotide misincorporations.
But no one has proposed anything OTHER than what you call "errors" for the ultimate source of the variety that the various mechanisms Shapiro alludes to reshuffle.

Bottom line:
You simply don't know what you're talking about.
2
... But the point is that without some imperfection in the reproduction process, i.e. without most, or at least some, offspring being unique, populations are doomed not to adapt. Which is why small populations tend to be vulnerable to extinction. Which is also why the Ark story is so bloody silly, but I do realise that the subtext here is that somehow you've got to get a lot of extra genetic variance into those animal pairs but you can't bring yourself to call them "errors".  But you won't get them from recombination either.  You need new alleles, which means that at least some of the gene sequences need to split and recombine mid-gene in a manner that will produce a gene different from both parents.  Some would call this an "error" in the recombination process.
This was the crux of the issue back in the "Who says Adam didn't have HUNDREDS of alleles?"  days, and Hawkins seems to have made no progress on it since.

Where DID the tens / hundreds / thousands of alleles per locus in animal genomes come from ?

Hint: Spoiler (click to show/hide)


I'm getting off Pingu's latest stupid merry go-round ...

But this from Voxrat is interesting ...

I will revisit it
Why did we even get off on the topic of error rates in DNA anyway?

:dunno:
Changed your mind, eh?

:badger:
3
In fact the whole Third Way movement got started because many scientists are finally beginning to realize this.
Nope.

Since you've never read a single book by any "Third Wayer" this, obviously, expresses nothing more than your wishful thinking.
4
And another 4 pages of David being obtusely and militantly wrong.

How do you suppose the sequences which are transfered via hgt arose?

Leprechauns?

The evidence indicates Special Creation initially.
You
believe this on faith alone because there is absolutely no evidence for this whatsoever.
5
And another 4 pages of David being obtusely and militantly wrong.

How do you suppose the sequences which are transfered via hgt arose?

Leprechauns?

The evidence indicates Special Creation initially.
No it doesn't.
6
Good Lord
Quote from: Dave Hawkins
Why do you waste the bandwidth to basically say "nuh uh"? Why don't you just use this post to explain yourself?
7
... But the point is that without some imperfection in the reproduction process, i.e. without most, or at least some, offspring being unique, populations are doomed not to adapt. Which is why small populations tend to be vulnerable to extinction. Which is also why the Ark story is so bloody silly, but I do realise that the subtext here is that somehow you've got to get a lot of extra genetic variance into those animal pairs but you can't bring yourself to call them "errors".  But you won't get them from recombination either.  You need new alleles, which means that at least some of the gene sequences need to split and recombine mid-gene in a manner that will produce a gene different from both parents.  Some would call this an "error" in the recombination process.
This was the crux of the issue back in the "Who says Adam didn't have HUNDREDS of alleles?"  days, and Hawkins seems to have made no progress on it since.

Where DID the tens / hundreds / thousands of alleles per locus in animal genomes come from ?

Hint: Spoiler (click to show/hide)


I'm getting off Pingu's latest stupid merry go-round ...

But this from Voxrat is interesting ...

I will revisit it
Hey! No hurry.
It's been 12 years.
What's another decade or three?
8
... But the point is that without some imperfection in the reproduction process, i.e. without most, or at least some, offspring being unique, populations are doomed not to adapt. Which is why small populations tend to be vulnerable to extinction. Which is also why the Ark story is so bloody silly, but I do realise that the subtext here is that somehow you've got to get a lot of extra genetic variance into those animal pairs but you can't bring yourself to call them "errors".  But you won't get them from recombination either.  You need new alleles, which means that at least some of the gene sequences need to split and recombine mid-gene in a manner that will produce a gene different from both parents.  Some would call this an "error" in the recombination process.
This was the crux of the issue back in the "Who says Adam didn't have HUNDREDS of alleles?"  days, and Hawkins seems to have made no progress on it since.

Where DID the tens / hundreds / thousands of alleles per locus in animal genomes come from ?

Hint: Spoiler (click to show/hide)

9
Fucking weasel Darwinists.

Dave, what you see as "weaselling" is simply what "Darwinists" always meant.  The fact that it turns out that you have always misunderstood it doesn't mean anyone has been trying to confuse you.  It means that you didn't pay enough attention or were too rigid to understand what they actually meant.
It could also mean he's never bothered to crack an introductory text on genetics.
10
DAVE'S DEFINITION OF "ERROR"

(AND AYALA'S ... AND EVERYONE ELSE'S EXCEPT PINGU)
Nope.

Show me any mainstream paper that agrees with your definition.

Sauce for the goose...
11
HGT is not considered an "error" ... Show me any mainstream paper that says it is ...

If you wanna talk about what real scientists consider to be "errors" read this that I've linked half a dozen times now ... https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409
That paper does not help you.
It simply defines "error" as inserting the "wrong" nucleotide(s).
Without defining "wrong".

But anyone with a high-school understanding of genetics understands it to mean: "different from the parental template", as I explained above.  HGT also results in progeny DNA different from the parental template.

Q.E.f.D.
12
I obviously know more about this one narrow topic than Pingu.
That is not "obvious" to anyone but you.
Quite the contrary, in fact.
13
This is your basic misunderstanding.
Your basic misunderstanding is thinking that you understand this stuff.

See: Dunning-Kruger effect.
14
You do NOT need a "non-zero error rate" to ensure long lineages in bacteria because of HGT.
You do not need HGT to ensure long lineages in bacteria.
15
For example, a human child IS a combination of half of the father's genes plus half of the mother's genes. 
Nope.
You still don't know what you're talking about.

So what is it you read between your "Adam had hundreds of alleles at each locus!!!1!" days and now that feeds the delusion that you now know more about the subject than the rest of us?
16
And I'm pretty sure that Pingu was referring to the latter when she was talking about a non zero error rate being a good thing for the purpose of making long lineages.
I'm pretty sure you're wrong.

Quote
What else could she possibly be talking about?
Clones.
17
Perfect recombination simply means that half of each parents genes are combined with no random errors like insertions or deletions or substitutions.

What else could it possibly mean?
Why is "half of each parents genes" more "perfect" than 40% of each parent's combining ?  :dunno:
Why would combining two individually neutral mutations - with no deletions or substitutions - to make a deleterious combination be considered "perfect" ?  :dunno:
18
I actually think I persisted in that error for only a few hours at which time I corrected it.
I actually think you're wrong.
I think the discussion is at AtBC, so if and when someone has the patience to deal with their search function, maybe we can see which of our memories is more accurate.
Quote
And that was 12 years ago. And yes I know a lot more now.
All without ever cracking an introductory genetics text!  Amazing.

Consider the possibility that you think you know a lot more. But actually don't.

Quote
Apparently I know a lot more than Pingu.
Apparently not.
19
I assumed she meant "perfect recombination" ... which living cells approach closely, but don't quite ever achieve.

If she didn't mean that, then WTH did she mean?
WTF do YOU mean?
What is "perfect recombination" supposed to mean?
What "living cells" approach it, whatever it is?
By what criteria do you judge how closely these "living cells" (whatever they are) approach it (whatever it is)?

You have no idea what you're talking about.
20
So make that Pingu ... AND Martin ... AND uncool ... that don't understand basic genetics.
Aaaaand ...
Here's Hawkins's signature totally inappropriate condescending  insulting bluster/bravado when trying to bluff his way through a subject in which he lacks the first clue.

No, Hawkins. It's YOU who doesn't understand basic genetics.

Remember how you went on for days (weeks? months?) condescendingly, insultingly, insisting that your biblical Adam and Eve must have had hundreds or thousands of alleles at every locus? 

:rofl:
:rofl::rofl:
:rofl::rofl::rofl:
:rofl::rofl::rofl::rofl:
:rofl::rofl::rofl::rofl::rofl:


Good times!  I suppose you would have us believe you've actually studied the subject since then, and now you've not only moved beyond such hilarious boners, your brilliant mind now runs circles around people who have studied molecular genetics all their lives.

Dave Hawkins:  poster child for militant ignorance
 
21
...
What we biochemists mean by "error" in nucleic acid polymerization is the incorporation of nucleotide(s) in the copy different from those in the template from which the copy is being made.

You're welcome.

VoxRat, PhD in Biochemistry.
Which includes, for example, reversions, right?
Yep
22
I refuse to entertain this perennial bullshit nonsense about copying errors in DNA not being mistakes. Utterly ridiculous and I refuse to waste my time.
How does a chemical reaction make a mistake?
By not copying the correct thing from the template. I don't know ... go ask a biochemist. It's them saying it, not me.
Thanks for asking.
What we biochemists mean by "error" in nucleic acid polymerization is the incorporation of nucleotide(s) in the copy different from those in the template from which the copy is being made.

You're welcome.

VoxRat, PhD in Biochemistry.
23
I refuse to entertain this perennial bullshit nonsense about copying errors in DNA not being mistakes. Utterly ridiculous and I refuse to waste my time.
:badger:
24
Of course it doesn't answer "the question" as to what DAVE means by "error". 

Dave himself doesn't even know what he means, any more than he knows what he means by "random".
I'm pretty sure it boils down to:
The sequence ordained by God is the "correct" sequence.
Copies of the sequence that differ from that are "incorrect", "mistakes", "errors"...
But, having just cited Shapiro, and written:
This is a science forum.
... he has to avoid honestly answering the question at all costs.

25
It could be a "mistake" or "error", I suppose.
Depending on your definition of "mistake" or "error".
What's yours? 

:icare:
Stupid ass question.

Read this ... https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409

Dave: try expressing what YOU think - your OWN point - instead of just linking to papers you clearly do not understand.
The linked paper, incidentally, does NOT answer the question.

I use expressions like "error-prone polymerase" all the time.
But, unlike Hawkins, I can tell you exactly what my definition of "error" is in that context.